


On Your Own

by CrazyForCsiMiami



Category: MacGyver (TV 2016)
Genre: Action/Adventure, Drama, Suspense
Language: English
Status: In-Progress
Published: 2020-04-28
Updated: 2020-06-11
Packaged: 2021-03-02 01:52:44
Rating: Not Rated
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 5
Words: 4,503
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/23886964
Author URL: https://archiveofourown.org/users/CrazyForCsiMiami/pseuds/CrazyForCsiMiami
Summary: Alternative look at Macgyver actually going Rogue
Relationships: Angus MacGyver & Desiree "Desi" Nguyen
Kudos: 2





	1. Chapter 1

“Macgyver has gone rogue!” Matty announced to the crowded war room where many agents were gathered alongside the remainder of the team. 

“I don’t understand why he’s doing this.   
I mean he hasn’t quite been himself lately but this is crazy!” Bozer insisted putting his hands on his head. 

“I’m not entirely sure but I wonder if having him explore his own mind may have pushed him over the edge considering the risks that came with it.” 

“Ok but without Mac what should we do?” Riley asked curiously. 

“That will depend on what intel we can get, right now I’m not completely certain that we all know what’s going on but Desi managed to plant a mic on him this morning in the event that he meets up with the head of codex.” 

“That’s right but for now I need everyone to check off everything on security protocol to prepare for another likely invasion if it comes to that.” Russ Taylor ordered. 

II

( Codex Facility) 

Macgyver walked into a room where his aunt Gwen was facing the window. 

“You actually came” 

“I’ve had a change of heart.” He vacillated 

Without moving she continued. “ You may be my nephew but how can I believe this after everything that’s happened?” 

He sighed. “ I can’t make you believe me but I’ve had a lot of time to think.” 

Gwen turned slowly towards him.   
“I need to be certain that you are no longer on the side of the phoenix foundation.” 

Mac shrugged. “ Just tell me what the next step is, I’m here to help.” 

She pulled up a picture on her phone and showed it to him. 

“Bring this girl from your former team to me.” 

Mac looked down toward the floor before returning his gaze to his aunt standing in front of him.   
“Ok but can I ask why?” 

Gwen smirked. “ I think with some time and training not only will she become like a niece I’ve never had but also a perfect codex operative.” 

She placed a finger to Mac’s chin. “ Do this and pledge your loyalty to the family business.” 

II 

(The War Room)

“ So it’s not good enough that she has grips on Mac, what’s next she’ll want Riley and Desi too?” Matty exclaimed. 

“Not surprising, codex has gotten desperate to find any means necessary to shut our operations down.” 

“I’m going to go warn Kara.” Matty put the tablet down.

“Wait, hang on let’s hold off on that.” Taylor suggested. 

“You have some kind of plan in mind?” 

“As a matter of fact I do.” Taylor walked around the room thinking while trying to explain his thought process at the same time. 

“ If Angus truly does not know how much we are aware of we need to use that to our advantage; we gotta make this look real.” He rubbed his facial hair. 

“Let him get in the door and attempt this but not allow him to get back out.” Taylor finished. 

Downstairs Macgyver had arrived back at the phoenix but he’s careful to watch his surroundings. 

After Mac goes out of sight from the main entrance Taylor stations himself there.   
“Riley, Bozer, Desi are you all in position?” 

“Affirmative.” Desi answers 

“Same here” Riley responded while peering around a corner. 

“Keeping an eye out down here.” Bozer replied. 

Angus eventually made his way to the war room, He stood for a moment observing Matty and Kara before proceeding with opening the door. 

Mac walked over and leaned down next to Kara. “Hey can we talk?” 

“Sure.” Kara placed the pen she was writing with down onto the table and rose up from the chair. 

Matty took a deep breath struggling not to say anything watching them leave the room. 

Once the door was shut she rushed over and tapped on the glass for privacy screens.   
“Taylor I hope you are ready down there.” 

( In the hallway) 

“ It’s a nice day we should go for a walk.” Mac Encouraged. 

“Sounds good.” She slid her hands into the jean pockets feeling hesitant but knowing this was a good opportunity to probe into what her friend was really feeling. 

Kara looked up and saw Taylor standing by the front doors and she smiled innocently. 

“Excuse us.” Macgyver motioned but Taylor didn’t budge. 

“I’m afraid I can’t move out of the way.” 

Macgyver stepped back. “Very funny, now if you don’t mind..” 

“Oh but I do mind.” Taylor objected 

Mac looked at Kara and back at Taylor. “Mind what, us going for a walk?” 

“Is that what you told her?” Taylor stepped closer to Mac 

“What’s going on?” Kara asked, noticing the rising tension. 

“Nothing, let’s just go.” Mac pressed, laying a hand on her shoulder and tried to side step away from Taylor only to be blocked again. 

Macgyver squared up. “ I would like to talk with Kara alone!” 

“Oh and what would that be that you would like to talk about, do you plan on revealing what your aunt has planned for her?!” Taylor’s face turned red as his anger was building.

“I don’t know what you’re talking about!” 

Taylor reached out and pulled Kara closer to himself. “This isn’t at all like you angus and I’m not sure what led to this but you’re out of your bloody mind if you think I’m going to let you turn anyone else here over to codex!” 

The heated conversation was interrupted when they both saw Gwen come inside. 

Taylor turned around swiftly and stood in front of Kara trying to shield her. 

“If you want her you’ll have to go through me first.” 

Without saying a word Gwen started to pull a gun from behind her back. 

“Kara go run!” Taylor spoke loudly while he reached out grabbing for the weapon. 

“Angus go after her!” His aunt demanded.


	2. Chapter 2

Running through the building with Mac close behind she couldn’t believe how fast things took an unbelievable turn and now Kara was being chased by someone she considered a good friend. 

As soon as some distance had been made between the two Kara ducked into a closet to try and deter him from where she had gone and placed her ear to the door trying to hear him go by. 

Macgyver stopped and looked around for a moment then continued down the hallway. 

Kara slowly peeked her head out and checked to see that the coast was clear and proceeded to take off in the other direction. 

Soon she made it to the war room quickly opening and shutting the door locking it then leaning against it trying to catch her breath. 

Matty looked up. “Kara...I..” 

Kara raised a hand up to her chest. “ Somethings…...wrong…..” She took a few more breaths.   
“He’s coming..” 

Her eyes widened when she heard the lock being tampered with so she dashed to the front of the room and stood next to Matty. 

Mac came into the room slowly and stopped for a moment giving a silent but cold stare. 

“Blondie think about what you’re doing, we can find a way to fix this.” Matty insinuated. 

“That’s what I’m trying to do now...fix everything.” Macgyver stated as he came in closer. 

Kara took a step back. “Mac please listen to me for a second.” She inhaled and glanced at Matty trying to work up her courage. 

“Things haven’t been right since you went head to head with your own mind, you know it, we all know it and it’s got you acting so out of whack as if you were someone else almost but I know the real you is still in there somewhere.” She looked at Matty again who nodded her head. 

“ You’re my friend Mac and I don’t plan on giving up on you, there has to be a way to get you back to normal, just let us try please.” 

Macgyver reached into his pocket. 

Matty and Kara smiled looking hopeful only changing their look when the zapping sound of a stun gun is heard. 

“I’m guessing that’s a no..” 

Mac lunges out towards her but she jumps back causing him to miss. 

She circles to the other side of the room pushing one of the chairs toward him before running out the door. 

(Downstairs) 

Taylor manages to knock the gun out of Gwen’s hand only to have her tackle him to the ground. 

“You’ll never be able to stop codex!” She throws down a punch. 

Taylor swipes his head out the way, Gwen’s fist hits the floor. 

The fight is interrupted when an alarm starts blaring throughout the building. 

Gwen smirks and lets go of Taylor’s shirt that she had twisted in her hands, she stands up and turns back leaning down to pick up the gun off the floor pointing it at him while she backs up to the entrance until she is able to open it and leave in a hurry. 

Taylor sits up, pushes himself off the floor and straightens his shirt out.   
“Riley what’s going on?” 

“Uh its not good, someone managed to break out the two we had in lock up.” she told him. 

“They couldn’t have made it far since we’ve been watching all the exits, just need to find them.” Desi encouraged. 

II

Kara came around a corner and spotted a set of double doors at the end of a corridor.   
“Phew.” 

“Uh-oh.” She thought when the doors didn’t budge. 

“Not now.” She continued trying to pull on the handles forcefully but it was no use. 

Footsteps approached from behind and she turned around knowing full well who it would be. 

Kara looked back and forth realizing she was trapped. 

She sighed. “Alright Mac you win, I’m not going to fight you, I know this isn’t your fault.” 

Kara closed her eyes accepting defeat; waiting for what was to come next. 

“No!” Desi shouted.

Kara opened her eyes looking up to see who had arrived. 

He peered over his shoulder, Desi promptly grabbed his arm that had been holding the stun gun and shoved it toward his neck. 

Macgyver collapsed onto the ground. 

Desi stepped over him and made quick work of tying up his arms and legs for once the effects wore off. 

“Are you ok?” Desi asked Kara as she stood up. 

“Yeah.” Kara nodded but did not take her eyes off Mac. 

Desi put an arm around Kara’s shoulders.   
“Don’t worry Bozer is researching to figure out what we can do to help him.” 

“What about Taylor?” Kara suddenly remembered. 

“He’s alright.” Desi assured. 

II

(Medical Bay) 

The team stood vigil watching and waiting for Macgyver to wake up after trying a potential treatment. 

“What if it doesn’t work?” Riley posed crossing her arms tightly. 

“We’ll cross that bridge if we get to it.” Matty replied. 

“I don’t have any doubts, this has been proven to be highly effective.” Bozer commented. 

Kara didn’t say a word, she was leaned over with her arms resting on the railings of the gurney. 

Taylor placed a hand on the small of her back trying to offer some comfort. 

She perked up when Macgyver moved his head and his eyes began to blink open. 

Desi reached out placing her hand in his and squeezed it gently.

“Hey guys..whats...what's going on?” He asked and began to sit up. 

Sighs of relief resounded throughout everyone. 

“Glad you’re back Mac.” Bozer stated. 

“Back?” He looked at each of them. “Back from where?” 

“What he means is, you’re you again.” Desi smiled widely and leaned down, giving him a kiss on the cheek. 

“Do you remember anything?” Taylor spoke up. 

"Not at all" He rubbed his eyes. 

"What happened?"

"You just weren't quite yourself that's all" Kara mentioned. 

"That would be an understatement, going all in for codex including your aunt using you to give Kara over to the cause." Matty explained. 

Macgyver began looking worried and confused. 

"Everything is fine though, nothing happened." Riley interjected. 

"That gives me an idea." Macgyver told them.


	3. Chapter 3

Everyone watched for a while as Taylor walked back and forth across the lab. 

“Why are you still pacing?” Riley shook her head. 

Taylor stopped and turned toward them. “Because I’m not feeling so strongly about this plan.” 

“ Think about it though, this is the best shot we’ve got against codex so far.” Bozer pointed out. 

“If you have any better ideas, we’re all ears.” Desi requested. 

“I don’t right now but I can't justify having just stopped what could have happened only to allow you Kara to walk right into codex’s hands!” Taylor declared throwing his hands in the air. 

“I hear what you’re saying, but this is a big opportunity, besides we still have the upper hand here.” Kara expressed. 

“Matty can’t you talk some sense into this?” He suggested. 

“I’m sorry Taylor but they’re not wrong, we don’t have a lot of options left so as long as the necessary precautions are put in place this team has to give it a shot.” She confessed. 

Taylor sighed. “Very well seeing as I appear to be outvoted here.” he walked up to Macgyver and made direct eye contact. 

“Angus I’m trusting you to keep your head out of the clouds on this and remember what’s at stake here.” 

“I think he gets it.” Riley interjected. 

II

(In The Car)

“You ok back there?” Mac looked over his shoulder briefly. 

“Yep.” Kara answered. 

“I’m really sorry about earlier.” He told her. 

“Mac you don’t have to be sorry, I don’t blame you for what happened; that’s why I was going to let you do it.” Kara revealed looking out the window. 

He furrowed his eyebrows. “What?” 

“I knew you weren’t too far gone so there was no way I would fight back and risk hurting you.” She shrugged. 

“You didn’t have to do that.” He gripped the wheel tighter. 

“Mac don’t start, I would endanger myself long before even possibly considering hurting someone I care about.” She reminded him. 

They soon arrived at the codex facility, after parking the car he leaned back and took a deep breath. 

“Remember my aunt knows as much about you as she does me so don’t try to convince her that you feel otherwise.” Mac clarified then stepped out of the car opening the back door. 

He helped her out of the back seat and held a grip on one of her arms since Kara’s hands were tied up behind her back. 

As both of them approached the building Gwen noticed from an indoor window and came outside. 

“Welcome back Angus.” She greeted and leaned down towards Kara. 

“She’s even adorable in person.” Gwen patted her on the head. 

Kara only scowled at her and Gwen turned around and signaled for Mac to follow.

She typed in a code on a keypad that opened a hidden access door leading to an elevator.

Kara attempted to pull away but was yanked back and pushed inside. 

A few seconds later the doors slid open to reveal a lively city below. 

“This is codex.” Gwen led the way. 

Kara let her jaw drop. “Woah..it’s like another world down here.” 

Mac looked around, seeing all the people and a flurry of activity. “Gotta tell you I definitely wasn’t expecting this.” 

“Marvelous isn’t it?” His aunt glowed. “Oh Scarlett, please take this one for now and put her in a cell.” she ordered the woman walking by. 

“I don’t think that’s necessary.” Macgyver disagreed. 

“Don’t worry, it's only until we are able to persuade her towards a new way of life, like you.” 

Kara stepped back before being grabbed by scarlett.   
“Let go!”   
She looked back wanting to so desperately call out for Mac to help but knowing she had to resist and protect the mission at hand. 

(The War Room) 

Signal Loss popped up on the screen. 

“How did we lose it?” Matty asked 

“I’m not sure, it shows they’re still at the ranch location.” Riley typed on the laptop vigorously. 

“I’ll try and boost it.” 

“Kara can you hear me?” She waited a moment. “Nothing, Taylor we’ve lost all contact.” 

(In A Van Remote Location) 

Taylor threw off his head set and bolted for the driver's seat. 

“What are you doing?!” Desi called out

“What do you think I’m doing? No communication means they are both at the mercy of codex so we need to get out there!” 

Desi reached over and blocked the steering wheel. “Except that we can’t codex doesn’t exactly have a welcome mat laid out for us!” 

“Matty we need a tag team!” He insisted. 

“Not yet Taylor we need to give Macgyver time to handle this.” 

“They both might not even have time!” 

“Be that as it may if we move in too soon it might blow Mac’s cover and could result in codex killing Kara, wait this out.” 

Taylor exhaled deeply and rubbed his eyes. 

(Codex Facility) 

“First order of business” Gwen showed him to a room with a big contraption in the center of it surrounded by many boxes. 

“What is this?” Macgyver slowly circled around looking it over. 

“Well I figured you could help us finish our new super weapon, considering the last one was destroyed.” 

Mac started sifting through the surrounding boxes observing all the various parts contained inside each one. 

“I’ll see what I can do.” He told her while holding up one of the parts. 

Gwen nodded. “Ok if you need anything just ask around, most people here know where to find me.” 

“Noted.” He answered.


	4. Chapter 4

"Will you at least release my hands?" Kara requested raising them up higher. 

*ugh I guess.." Scarlett reached down and pulled the ropes loose letting it drop to the floor before opening the door to the cell and pushing Kara forward. 

" Do I get bathroom breaks or?.." 

Scarlett ignored the question. "Enjoy your new home." She stated and took off down the hallway. 

"Ok nice talking to you." Kara spoke sarcastically while sliding down the wall to sit on the hard floor. 

II

Russ, Desi and Riley pulled up to the ranch location building and got out of the car. 

With weapons drawn they approached the doors. 

Russ signaled and pulled one open and took the lead going inside. 

He stopped and looked around before putting the weapon away. 

"Empty?" Desi said, feeling surprised.

Riley looked down at the tablet in her hands. 

" I don't get it, the location shows them being here and never moved." 

"This whole place is deserted, none of it makes any sense." Russ Exclaimed putting one hand to his side and rubbing his chin with the other and began pacing trying to think. 

"Matty what do we do?" Desi asked. 

"For the moment all of you come back to the Phoenix, right now we are just gonna have to wait for Mac or Kara to reestablish contact." 

II

(Codex Underground) 

Scarlett stood in the doorway watching as Mac worked on the super weapon before approaching him. 

"So tell me a little more about yourself." She stated. 

With his back still towards her, he rolled his eyes. 

"You mean my aunt hasn't already laid it all out for you?" 

"She doesn't exactly divulge that stuff to just anyone here." Scarlett crossed her arms. 

Mac put down the wrench he was holding and turned towards her leaning back against the machine. 

"Not sure there's much to tell, I like the deeper parts of math and science that most people give blank stares to, I can make stuff out of random things, and I now think all of this." He paused 

"has some sort of reasoning to it." 

She nodded her head and moved closer observing the weapon being built. 

"Is this going to be ready for today then?" She probed. 

"I suppose if it's needed that soon but my aunt wasn't clear on a timeline."   
He picked up the wrench and got back to work on it. 

"Plans have changed since your arrival. We knew you could help speed things up.” 

“In that case if you don’t mind I kind of need to focus.” Mac picked up a few more pieces and attached them. 

“Understood, we’ll talk later.” Scarlett placed her hands into her pockets and backed away a few steps, she looked over at him once more before leaving the room. 

II

"Listen up everyone!" Gwen stepped onto a platform in front of a growing crowd of codex operatives. 

She looked around to ensure everyone was at attention.   
"The time has finally come, thanks to the hard work of my ingenious nephew Angus Macgyver we can put the plans everyone has spent so much time working on into action." 

Applause sounded throughout the room.   
"Each of you have your assigned routes and the time of the meet up."   
“Together we can still save the earth from ultimate demise!” Gwen raised her fist and the air and watched as everyone else did the same. 

Just as the crowd started to disperse, Mac approached with hands in his pockets. 

Gwen stepped down and went right up to him.   
‘“Are you ready for this?” 

“I guess it's time” He remarked. 

“Great, let’s go!” She grinned, patting his arm. 

“Wait what about Kara?” Mac remembered pointing toward the direction of the corridor. 

“What about her?” Gwen asked, looking confused. 

Mac tilted his head. “If you really want to convince her toward the cause then we need to bring her with us.” 

Gwen sighed. “After this happens Kara won’t have much of a choice regardless.” 

“Without seeing it first hand she’ll still oppose it, what do we have to lose by taking her?” He narrowed his eyes at Gwen waiting for an answer. 

Gwen looked at the ground scuffing her feet for a moment thinking about it. 

“You seem to feel strongly about this...I’ll trust you.”


	5. Chapter 5

"Wake up" Her eyes snapped open hearing those words from a familiar voice.

He typed in a code on the keypad, opened the door then walked inside and reached out a hand towards her. 

Kara grabbed his hand letting him help her up.   
"You good?" 

"Yeah I'm fine, are we going home now?" 

"Not quite yet but we are going somewhere." 

II 

The rest of the team was gathered in the war room waiting anxiously to have any contact when an alert came up on the screen. 

Riley picked up the tablet. "They're on the move again." 

Russ pointed to the screen. "This shows them heading down highway 191." 

"That leads straight to Yellowstone national park, why would codex need to go there?" Desi questioned. 

"Either way the reason can't be good, I'm sending tag teams. Desi, Russ and Riley if you head out now there is a chance to get there first and stop whatever plan codex has in mind." Matty instructed. 

II 

(HIGHWAY 191)

Gwen was driving the three row seated truck with Kara beside her in the middle and Macgyver on the other side. 

"So where are we headed exactly?" Kara pointed her eyes back and forth. 

"Yellowstone National Park." Gwen stated 

"In that case I hope there will be time for sight seeing since I've never been there, we should also go to the gift shop and browse the trinkets; hopefully they have nice keychains with the names on them and I wonder what animals will be there and.." Kara rambled on. 

"Just stop ok!" Gwen squeezed the steering wheel becoming frustrated. 

Kara looked at Mac. "Guess you forgot to warn her about my chatterbox tendencies huh?" 

"She turned her head again. "Fun fact aunty Gwen, when I get on a roll I hardly ever shut up." 

Gwen shook her head. "Here I thought you said we had nothing to lose Angus." 

“Just give it time, you’ll adjust.” Mac stated using his aunt’s own words towards her. 

“Touche.” She spouted back. 

Before much longer they arrived, Gwen parked the truck and stepped out taking a big deep breath staring at the horizon. 

“Here we are.” Gwen clasped her hands and looked back. 

“Can I go to the bathroom?” Kara requested giving an innocent look. 

Gwen sighed. “I suppose, Keep an eye on her Angus.” 

Mac put his arm around Kara’s shoulders and led her away. 

“What now?” Kara whispered looking up at him. 

“You still have your cell phone?” He asked lowley. 

“Yeah, Scarlett didn’t bother to search me thankfully.” 

Mac looked over his shoulder to make sure no one followed before raising his voice to a normal level once they were far enough away. 

“ While you’re in there, text Matty and Russ, get them up to speed because we need to act now.” 

“Got it and one other thing?” Kara stopped to make eye contact. 

“What’s that?” 

“Try not to let your aunt pat me on the head again, my hands aren’t tied up anymore so I don’t promise any self restraint.” Kara made a fist and pushed it into the other hand. 

“Understood.” Mac nodded.   
II

“Riley you go find Mac and Kara, Desi and I will give codex a little greeting.” Russ instructed once the three of them got out of the car. 

Riley rushed toward the building following the direction the tablet was showing the red dot locations leading to.

Russ and Desi got closer to the gathering that had started to build and hid behind a few vehicles to avoid being seen. 

“Looks like they have a new super weapon.” Desi noticed watching the men unload it from the back of the pickup truck. 

“Question is what do they intend to use it for?” 

“I say we don’t give them anytime to show off.” Desi started to get up but Russ grabbed onto her arm pulling her back. 

“We can’t take them yet while still outnumbered largely!” 

“There isn’t much time left!” Desi insisted. 

“I’m well aware of that.” Russ placed a hand over his ear. “Riley hurry.” 

II

While waiting for Kara, Mac saw some of the display cases in the gift shop and started to browse. 

Riley came in and took another glance at the tablet making sure she was in the right spot before heading towards the ladies restroom and going inside. 

“Kara are you here?” She called out carefully. 

Riley looked around. 

Kara opened the stall door and peeked out. “Riley!” she swung it open the rest of the way

Both of them rushed into a hug. 

"Where have you guys been?  
The ranch location was deserted and we worried when your coms went out." 

Kara stepped back to lean against the sink counter. 

"Codex is much bigger than any of us anticipated, they have like this whole underground city."   
She explained while staring off remembering what they saw. 

“Do you know their plan?” Riley asked. 

“No, the only thing I’m certain of is they had Mac help build a new superweapon, the possibilities are endless.” 

While they were catching up someone entered inside not catching either of their attention until the click of a gun trigger sounded. 

Both raised their hands up. “Busted.”


End file.
